M&A can be divided into two different types, one is related transaction and another is non affiliated transaction. For the two different types of M&A, the paper analyzes the impact of the company’s ownership structure on firm performance based on panel data of 200 manufacturing listed companies from 2009 to 2013 in China. It shows that, in non affiliated transaction affairs, the majority shareholder ratio of the company is significantly positively correlated with the short term company performance, while the majority shareholder ratio of the company is significantly negative correlated with the long term company performance. In non affiliated transaction affairs, the equity restriction ratio of the company is significantly positively correlated with the short term company performance, while the equity restriction ratio of the company is significantly negative correlated with the long term company performance. In both types of M&A, the attribute of the actual controller of the company is significantly uncorrelated with the company performance.